Variant report

Variant	rs12194640
Chromosome Location	chr6:16757969-16757970
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:16756701-16760622	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:16756434-16758301	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:16756699-16762336	K562	blood:	n/a	n/a
4	EBF1	chr6:16757587-16758024	GM12878	blood:	n/a	chr6:16757855-16757866 chr6:16757816-16757827 chr6:16757816-16757829
5	TCF7L2	chr6:16756655-16758309	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:85592923..85596255-chr6:16757225..16759434,3	K562	blood:
2	chr6:16690235..16693001-chr6:16757238..16760223,2	MCF-7	breast:
3	chr6:16738386..16740678-chr6:16757048..16758889,2	MCF-7	breast:
4	chr6:16713714..16716602-chr6:16757924..16759953,2	MCF-7	breast:
5	chr14:81686384..81688841-chr6:16756880..16759563,2	MCF-7	breast:

Variant related genes	Relation type
ATXN1	TF binding region
ENSG00000229931	TF binding region
ENSG00000165417	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10434861	0.86[CEU][hapmap]
rs10456788	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs10456789	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs10456790	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs16878970	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs16879003	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs16879071	1.00[YRI][hapmap]
rs3806144	0.86[CEU][hapmap]
rs6459484	0.86[CEU][hapmap]
rs9350015	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16737600-16759400	Weak transcription	Thymus	Thymus
2	chr6:16741200-16758200	Enhancers	Fetal Heart	heart
3	chr6:16743000-16759600	Weak transcription	Spleen	Spleen
4	chr6:16745000-16759600	Weak transcription	Placenta	Placenta
5	chr6:16746200-16758400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:16746400-16758600	Weak transcription	Primary T cells from cord blood	blood
7	chr6:16746400-16758800	Weak transcription	Fetal Thymus	thymus
8	chr6:16746800-16758600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:16748200-16758200	Weak transcription	Brain Germinal Matrix	brain
10	chr6:16748200-16758400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:16748400-16758000	Weak transcription	Fetal Brain Female	brain
12	chr6:16748800-16758400	Weak transcription	Gastric	stomach
13	chr6:16748800-16758600	Weak transcription	Right Atrium	heart
14	chr6:16748800-16758800	Weak transcription	Ovary	ovary
15	chr6:16748800-16759000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:16748800-16759800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:16749200-16758400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:16750200-16758600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:16750400-16758600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:16750400-16758800	Weak transcription	Esophagus	oesophagus
21	chr6:16750400-16759800	Weak transcription	Lung	lung
22	chr6:16750600-16759000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:16752200-16758600	Enhancers	Colon Smooth Muscle	Colon
24	chr6:16752400-16758600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:16752800-16758400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:16752800-16758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:16752800-16758800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:16753200-16758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:16753200-16758600	Weak transcription	Pancreas	Pancrea
30	chr6:16753400-16758200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:16753400-16758400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:16753400-16758600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:16753600-16758200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:16753600-16758400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:16753600-16758400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:16753600-16758400	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:16753600-16758400	Weak transcription	NHLF	lung
38	chr6:16753600-16758600	Weak transcription	Left Ventricle	heart
39	chr6:16753600-16758800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:16753600-16758800	Enhancers	Fetal Intestine Small	intestine
41	chr6:16753600-16759200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:16753800-16758400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:16753800-16758400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:16753800-16758600	Weak transcription	Fetal Stomach	stomach
45	chr6:16753800-16758600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:16753800-16759000	Weak transcription	HUVEC	blood vessel
47	chr6:16753800-16759200	Weak transcription	Aorta	Aorta
48	chr6:16754000-16758000	Weak transcription	Brain Substantia Nigra	brain
49	chr6:16754000-16758600	Weak transcription	HSMM	muscle
50	chr6:16754800-16758800	Enhancers	HepG2	liver

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